I was wondering if AxPyMOL could handle a .pse file that loaded two pdb
structures in powerpoint.
I've simply created a .pse file by fetching 2bmv and 2hhb. Then I loaded this
onto my PC laptop while in powerpoint. Other slides in the same presentation
with a single pdb file works fine. However, this .pse file causes AxPyMOL to
crash.
Any tips or suggestions would be greatly appreciated!
Thanks in advance.
Sean
> From: pymol-users-requ...@lists.sourceforge.net
> Subject: PyMOL-users Digest, Vol 39, Issue 4
> To: pymol-users@lists.sourceforge.net
> Date: Tue, 11 Aug 2009 21:41:44 +0000
>
> Send PyMOL-users mailing list submissions to
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>
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> or, via email, send a message with subject or body 'help' to
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> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of PyMOL-users digest..."
>
>
> Today's Topics:
>
> 1. Re: de-speculating? (Thomas Stout)
> 2. figure of buried surface area (Jiamu Du)
> 3. Re: figure of buried surface area (Shiven Shandilya)
> 4. Measure surface area (Mirek Cygler)
> 5. Re: Measure surface area (Warren DeLano)
> 6. Re: Measure surface area (Robert Campbell)
> 7. accidently used appearance wizard, and lost my selected
> sidechaine (David Shin)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 7 Aug 2009 15:54:24 -0700
> From: "Thomas Stout" <tst...@exelixis.com>
> Subject: Re: [PyMOL] de-speculating?
> To: "Warren DeLano" <war...@delsci.com>,
> <pymol-users@lists.sourceforge.net>
> Message-ID:
> <c5f9061847b41144899dc5637aef2d22afb...@excl01.exelixis.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
>
> Thanks very much, Warren. Perhaps I've dorked something in my other
> settings, but I'm getting rather horrid results even with your suggestions;
> I'm going to start with a fresh session and see....
>
> -Tom
>
> PS - I'm "trapped" in CYMK color space since this is a job for a printing
> house....
>
> -----Original Message-----
> From: Warren DeLano [mailto:war...@delsci.com]
> Sent: Fri 8/7/2009 3:08 PM
> To: Thomas Stout; pymol-users@lists.sourceforge.net
> Subject: RE: [PyMOL] de-speculating?
>
> Hi Tom,
>
>
>
> set specular, 0
>
>
>
> alone should be enough to do the job if all you want to do is turn off
> specular lighting -- you can ignore all those other spec_* settings.
>
>
>
> However, for a more matte appearance I'd be more inclined to try:
>
>
>
> set shininess,10
>
>
>
> set specular_intensity, 0.2
>
>
>
> # and perhaps
>
>
>
> space pymol
>
>
>
> # in order to lessen problems with color saturation.
>
>
>
> Cheers,
>
> Warren
>
>
>
> ________________________________
>
> From: Thomas Stout [mailto:tst...@exelixis.com]
> Sent: Friday, August 07, 2009 2:51 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] de-speculating?
>
>
>
>
>
> Hi All --
>
>
>
> Would anyone happen to have a "recipe" handy for turning down/off the
> specularity (of CPK spheres especially) in PyMOL? I happen to be a fan
> of more "matte" surfaces and find the highlights to be rather extreme.
> I've been messing around with all of the parameters as found on
> PyMOLwiki:
>
>
>
> Spec direct
>
> Spec direct power
>
> spec power
>
> specular
>
> specular intensity
>
>
>
> as well as
>
> reflect
>
> ambient
>
>
>
> et cetera
>
>
>
> but haven't really found the sweet spot.
>
>
>
> My current settings look like:
>
> spec_count, 1
>
> spec_direct, 0.0
>
> spec_direct_power, 2000
>
> spec_power, 2000
>
> spec_reflect, 2
>
> specular, 0
>
> specular_intensity, 0.5
>
> ambient, 0.08
>
> reflect, 0.66
>
>
> This is close, but loses some dimensionality in the CPK spheres (they
> now look flat in the middle). Oddly, the spheres look great in the GUI
> (unrendered) but the ray-traced version seems to clip the shading/color
> distribution badly....
>
>
>
> Any suggestions?
>
>
>
> Thanks!
>
> -Tom
>
>
>
>
>
> This email (including any attachments) may contain material
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> contact the sender and delete all copies.
> Exelixis, Inc. reserves the right, to the extent and under
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>
> This email (including any attachments) may contain material
> that is confidential and privileged and is for the sole use of
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> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 2
> Date: Sun, 9 Aug 2009 11:09:48 +0800
> From: Jiamu Du <jiam...@gmail.com>
> Subject: [PyMOL] figure of buried surface area
> To: Pymol <pymol-users@lists.sourceforge.net>
> Message-ID:
> <ebbefa6c0908082009q5f7d0f3ejbaeed9c03fb37...@mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Pymol BBSers,
> I want to generate a figure to show the overlap of two binding epitopes.
> Both two proteins A and B can interact with protein C, while their binding
> epitopes on C are overlapped. So I want to generate a figrue as this: the
> surface of protein C is colored as white, the buried surface area of A on C
> is colored as red, the buried surface area of B on C is colored as yellow,
> and the overlapped region is colored as orange. I tried several time, all
> the figures are not so beautiful. Is there anyone who can perform this well?
>
> Thanks and best wishes.
>
>
> --
> Jiamu Du, Ph.D.
> State Key Laboratory of Molecular Biology
> Institute of Biochemistry and Cell Biology
> Shanghai Institutes for Biological Sciences
> Chinese Academy of Sciences
> 320 Yue-Yang Road
> Shanghai 200031
> P. R. China
> Tel: +86-21-5492-1117
> E-mail: jiam...@gmail.com
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 3
> Date: Sun, 9 Aug 2009 00:02:39 -0400
> From: Shiven Shandilya <shiven.shandi...@gmail.com>
> Subject: Re: [PyMOL] figure of buried surface area
> To: Jiamu Du <jiam...@gmail.com>
> Cc: Pymol <pymol-users@lists.sourceforge.net>
> Message-ID:
> <12f23f7b0908082102j2b274a2fn7d0a7e4fab64a...@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Jiamu,
>
> Have you looked at VASCo :
>
> http://genome.tugraz.at/VASCo/
>
> I have found it to be very useful and very capable. Contact
> interfaces, electrostatics (with Delphi) and many other features are
> available. And best of all, it works extremely well with PyMOL.
>
> Do read the manual carefully and you should be able to get very high
> quality surface images with a little tweaking.
>
> Best,
> Shiven
>
>
>
> On Sat, Aug 8, 2009 at 11:09 PM, Jiamu Du<jiam...@gmail.com> wrote:
> > Dear Pymol BBSers,
> > I want to generate a figure to show the overlap of two binding epitopes.
> > Both two proteins A and B can interact with protein C, while their binding
> > epitopes on C are overlapped. So I want to generate a figrue as this: the
> > surface of protein C is colored as white, the buried surface area of A on C
> > is colored as red, the buried surface area of B on C is colored as yellow,
> > and the overlapped region is colored as orange. I tried several time, all
> > the figures are not so beautiful. Is there anyone who can perform this well?
> >
> > Thanks and best wishes.
> >
> >
> > --
> > Jiamu Du, Ph.D.
> > State Key Laboratory of Molecular Biology
> > Institute of Biochemistry and Cell Biology
> > Shanghai Institutes for Biological Sciences
> > Chinese Academy of Sciences
> > 320 Yue-Yang Road
> > Shanghai 200031
> > P. R. China
> > Tel: +86-21-5492-1117
> > E-mail: jiam...@gmail.com
> >
> > ------------------------------------------------------------------------------
> > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> > trial. Simplify your report design, integration and deployment - and focus
> > on
> > what you do best, core application coding. Discover what's new with
> > Crystal Reports now. ?http://p.sf.net/sfu/bobj-july
> > _______________________________________________
> > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> >
>
>
>
> --
> ~^v^~ the cgull ...
>
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 10 Aug 2009 13:47:52 -0400
> From: "Mirek Cygler" <mi...@bri.nrc.ca>
> Subject: [PyMOL] Measure surface area
> To: <pymol-users@lists.sourceforge.net>
> Message-ID: <53cf8c3c7e9049bbb685c6a69809b...@pcmsg28>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi,
> How can I get the measure in A2 of the surface area of the surface I
> display with PyMol?
>
> Mirek
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 10 Aug 2009 11:21:39 -0700
> From: "Warren DeLano" <war...@delsci.com>
> Subject: Re: [PyMOL] Measure surface area
> To: <mi...@bri.nrc.ca>, <pymol-users@lists.sourceforge.net>
> Message-ID:
> <896b75251ba19745a529b1b867893fa50eb...@planet.delsci.local>
> Content-Type: text/plain; charset="us-ascii"
>
> Mirek,
>
> PyMOL isn't the optimal tool for measuring surface area -- perhaps
> others on the list can suggest good alternatives.
>
> The only kind of surface area PyMOL can measure well is solvent
> accessible area, and it is a bit slow because all it does is sum up
> partial areas associated with discrete dots on spheres (size = vdw +
> solvent radius). The basic approach is:
>
> # (1) make sure no atoms are ignored:
>
> flag ignore, none
>
> # (2) delete everything except what you want to measure (important!):
>
> remove not polymer
>
> # (3) adjust dot settings for solvent surface area measurement:
>
> set dot_solvent, on
>
> set dot_density, 4
>
> # (4) visually preview what is being measured (optional):
>
> show dots
>
> # (5) computer the surface area value:
>
> print cmd.get_area()
>
> Cheers,
> Warren
>
>
> > -----Original Message-----
> > From: Mirek Cygler [mailto:mi...@bri.nrc.ca]
> > Sent: Monday, August 10, 2009 11:08 AM
> > To: pymol-users@lists.sourceforge.net
> > Subject: [PyMOL] Measure surface area
> >
> > Hi,
> > How can I get the measure in A2 of the surface area of the
> surface I
> > display with PyMol?
> >
> > Mirek
> >
> >
> >
> ------------------------------------------------------------------------
> --
> > ----
> > Let Crystal Reports handle the reporting - Free Crystal Reports 2008
> 30-
> > Day
> > trial. Simplify your report design, integration and deployment - and
> focus
> > on
> > what you do best, core application coding. Discover what's new with
> > Crystal Reports now. http://p.sf.net/sfu/bobj-july
> > _______________________________________________
> > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives:
> http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> >
> >
> >
>
>
>
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 10 Aug 2009 14:49:06 -0400
> From: Robert Campbell <robert.campb...@queensu.ca>
> Subject: Re: [PyMOL] Measure surface area
> To: pymol-users@lists.sourceforge.net
> Message-ID: <20090810144906.275fd...@adelie.biochem.queensu.ca>
> Content-Type: text/plain; charset=US-ASCII
>
> Hi Mirek,
>
> On Mon, 10 Aug 2009 11:21:39 -0700 Warren DeLano <war...@delsci.com> wrote:
>
> > PyMOL isn't the optimal tool for measuring surface area -- perhaps
> > others on the list can suggest good alternatives.
>
> I like MSMS for this. I have a script that will calculate the area (both
> solvent exposed and solvent accessible) for a particular selection.
>
> See my msms_pymol.py script at:
>
> http://pldserver1.biochem.queensu.ca/~rlc/work/pymol
>
> After loading the script with the "run" command, you can type "help
> calc_msms_area" to get more information on the options.
>
> Cheers,
> Rob
> --
> Robert L. Campbell, Ph.D.
> Senior Research Associate/Adjunct Assistant Professor
> Botterell Hall Rm 644
> Department of Biochemistry, Queen's University,
> Kingston, ON K7L 3N6 Canada
> Tel: 613-533-6821 Fax: 613-533-2497
> <robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc
>
>
>
> ------------------------------
>
> Message: 7
> Date: Tue, 11 Aug 2009 14:41:25 -0700 (PDT)
> From: David Shin <dav...@scripps.edu>
> Subject: [PyMOL] accidently used appearance wizard, and lost my
> selected sidechaine
> To: pymol-users@lists.sourceforge.net
> Message-ID: <alpine.osx.1.10.0908111438400.18...@alkb.scripps.edu>
> Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII
>
> Hi
>
> I was about to draw a bond between a sidechain (that was represented using
> "select", not "create", using the measurement wizard. I pulled down that
> appearance wizard by mistake, and clicked on the sidechain. It
> disappeared. Anyone have a clue how to get it back? Going to the selection
> and pulling down show sidechain doesn't seem to work.
>
> I did a few google searches, and tried the wiki, but no luck.
>
> Thanks,
>
> Dave
>
>
>
> ------------------------------
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now. http://p.sf.net/sfu/bobj-july
>
> ------------------------------
>
> _______________________________________________
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
> End of PyMOL-users Digest, Vol 39, Issue 4
> ******************************************
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